A specialty pharmacy has clinicians trained in certain disease states, such as palliative care, HIV, transplant, oncology and some are beginning to work with health conditions like diabetes. They typically work with a high cost or high complexity disease state in the hopes of improving are for those patients.

The pharmacists at the specialty pharmacies will have the applicable education and/or certification for disease state management and will have greater knowledge of drug treatments, interactions, management of those interactions, toxicities, adverse reactions, etc for that particular disease state. While hopefully any medication error will be spotted at any pharmacy, the odds are increased if the pharmacist is intimately familiar with that particular disease state, dispenses many prescriptions for those medications, and knows the prescribing habits of local physicians. They also may or may not compound (mix up) special dosage forms of medications like topical gels or suppositories for medications not commercially available in those dosage forms. In addition, specialty pharmacies will stock all drug therapies for that disease state, rather than the local pharmacy having to special order them.

I'm not certain why the oncologist is recommending a specialty pharmacy in your case- perhaps he has a good relationship with the staff there, perhaps he commonly prescribes specially compounded medications, perhaps the pharmacists are more opiate-friendly (pain medications), or you live in an area where the local pharmacy does not stock commonly used items, etc. Some of these pharmacies will also provide the doctor with patient compliance data (did they refill on time, meaning they likely took their meds as prescribed), which can be especially useful in post-transplant or HIV treatments.